COVID-19 Dynamics & Evolution - Part 2

October 19-20, 2020

This meeting will feature cutting-edge research on COVID-19 epidemiology, modeling, and evolution selected from abstracts submitted by the scientific community.

AGENDA | POSTERS | COURSE CHAIRS | SYLLABUS

Agenda

Draft Agenda (all times are relative to start time of 06:00 Pacfic Daylight Time, UTC-7)

Monday, October 19, 2020
Session 1 - Epidemiology of COVID-19 
Session Chairs:  Benjamin Rader & Michael Levy
6:00 AM Welcome & Introductions
6:10 AM THE ROLE OF BEHAVIOR, MOBILITY, AND SOCIAL NETWORKS IN SHAPING THE COVID-19 PANDEMIC, *Sam Scarpino
6:30 AM LOCALIZED END-OF-OUTBREAK DETERMINATION FOR COVID-19: EXAMPLES FROM CLUSTERS IN JAPAN, *Natalie Linton
6:45 AM IMPROVED ESTIMATION OF TIME-VARYING REPRODUCTION NUMBERS AT LOW CASE INCIDENCE AND BETWEEN EPIDEMIC WAVES, *Kris Parag
7:00 AM PRE-SYMPTOMATIC TRANSMISSION OF SARS-COV-2 IN CHINA: BEFORE AND AFTER THE LOCKDOWN, *Mary Bushman
7:15 AM GENOMIC EPIDEMIOLOGY APPROACH TO ESTIMATING THE SERIAL INTERVAL DISTRIBUTION, *Kurnia Susvitasari
7:30 AM REVEALING THE EXTENT OF THE COVID-19 PANDEMIC IN KENYA BASED ON SEROLOGICAL AND PCR-TEST DATA, *Samuel Brand
7:45 AM ESTIMATING COVID-19 SECONDARY ATTACK RISK IN ELDERLY CARE FACILITIES IN FRANCE, *Bastien Reyné
8:00 AM ESTIMATING CUMULATIVE INCIDENCE OF SARS-COV-2 WITH IMPERFECT SEROLOGICAL TESTS: EXPLOITING CUTOFF-FREE APPROACHES, *Judith Bouman
8:15 AM Break
Session 2 - Characterizing SARS-CoV2-Evolution
Session Chairs: Sarah Nadeau & Jan Albert
8:30 AM NATURAL SELECTION IN THE EVOLUTION OF SARS-COV-2 IN BATS, NOT HUMANS, CREATED A HIGHLY CAPABLE HUMAN PATHOGEN, *Sergei Pond
8:45 AM CHARACTERISING SARS-COV-2 WITHIN-HOST DIVERSITY AND IMPLICATIONS FOR RESOLVING TRANSMISSION, *Matthew Hall
9:00 AM DECOMPOSING THE SOURCES OF SARS-COV-2 FITNESS VARIATION IN THE UNITED STATES, *David Rasmussen
9:15 AM THE CONTRIBUTION OF MUTATION AND SELECTION TO PARALLEL EVOLUTION IN CIRCULATING LINEAGES OF SARS-CoV-2, *Luz Angela Alonso-Morales
9:30 AM Break
Session 3 - Modeling SARS-CoV-2 epidemic control
Session Chairs: Dan Reeves & Cecile Vibound
9:45 AM DRIVERS OF RESURGENT COVID-19 EPIDEMICS IN THE UNITED-STATES: SITUATION ANALYSIS THROUGH AUGUST 23 BASED ON AGE-SPECIFIC MORTALITY DATA AND AGE-SPECIFIC MOBILITY DATA AT STATE LEVEL, *Mélodie Monod
10:00 AM QUANTIFYING POPULATION CONTACT PATTERNS IN THE UNITED STATES DURING THE COVID-19 PANDEMIC, *Ayesha Mahmud
10:15 AM A SIMPLE CRITERION TO DESIGN OPTIMAL NON-PHARMACEUTICAL INTERVENTIONS FOR EPIDEMIC OUTBREAKS, *Marco Tulio Angulo
10:30 AM AGE-STRUCTURED NON-PHARMACEUTICAL INTERVENTIONS FOR OPTIMAL CONTROL OF COVID-19 EPIDEMIC, *Ramses Djidjou-Demasse
10:45 AM TESTING, TRACING AND ISOLATION IN COMPARTMENTAL MODELS, *Jasmina Panovska-Griffiths
11:00 AM Break
Session 4 - Forecasting SARS-CoV-2 spread  
Session Chairs: Ruian Ke & Ramsès Djidjou-Demasse
11:15 AM REAL-TIME PROJECTIONS OF COVID-19 IN THE UNITED STATES, *Sen Pei
11:27 AM PROJECTING COVID-19 SPREAD AND MORTALITY USING RIDGE REGRESSION, *Sabrina Corsetti
11:39 AM PREDICTABILITY: CAN THE TURNING POINT AND END OF AN EXPANDING EPIDEMIC BE PRECISELY FORECAST WHILE THE EPIDEMIC IS STILL SPREADING? *Mario Castro  
11:51 AM THE RISK FOR A SECOND WAVE, AND HOW IT DEPENDS ON R0, THE CURRENT IMMUNITY LEVEL AND PREVENTIVE MEASURES, *Tom Britton
12:03 PM THE EFFECT OF EVICTIONS ON THE TRANSMISSION OF SARS-COV-2,*Justin Sheen
12:15 PM Closing Remarks
Tuesday, October 20, 2020
6:00 AM Welcome and Introductions
Session 5 - Modeling SARS-CoV-2 vaccination
Session Chairs: Jasmina Panovska-Griffiths & Laura Matrajt Arbetman
6:10 AM THE IMPACT OF COVID-19 RACIAL AND ETHNIC DISPARITIES ON HERD IMMUNITY THRESHOLDS AND OPTIMAL VACCINE ALLOCATION STRATEGIES, *Kevin Ma
6:25 AM A VACCINE THAT IS NOT FULLY PROTECTIVE, BUT INDUCES A SMALL REDUCTION IN PEAK SARS-COV-2 VIRAL LOAD AMONG INFECTED PEOPLE, COULD DECREASE INFECTIOUSNESS AND REDUCE INCIDENT INFECTIONS AND DEATHS, *Josh Schiffer
6:40 AM DIFFERENTIAL SOCIAL DISTANCING AND SARS-CoV-2 VACCINE HESITANCY BY INFLUENZA VACCINATION STATUS IN THE UNITED STATES, *Benjamin Rader
6:55 AM EXPLORING POSSIBLE SCENARIOS FOR THE COVID-19 VACCINATION PROGRAM IN JAPAN, *Sung-Mok Jung
7:10 AM MODEL-INFORMED COVID-19 VACCINE PRIORITIZATION STRATEGIES BY AGE AND SEROSTATUS, *Kate Bubar
7:25 AM DYNAMIC PRIORITIZATION OF SCARCE COVID 19 VACCINES, *Jack Buckner
7:40 AM Break
Session 6 - Phylogenetics of SARS-CoV-2 Around the World
Session Chairs: Aine O'Toole & Danielle Miller
7:55 AM THE EMERGENCE OF SARS-COV-2 IN EUROPE AND NORTH AMERICA, *Mike Worobey
8:10 AM TRACKING THE INTRODUCTION AND SPREAD OF SARS-COV-2 IN COASTAL KENYA *George Githinji
8:25 AM INSIGHTS INTO THE EVOLUTION AND EPIDEMIC SPREAD OF SARS-COV-2 IN SWITZERLAND THROUGH A LARGE-SCALE SEQUENCING EFFORT, *Tanja Stadler
8:40 AM PHYLOGENETIC ANALYSIS OF THE TIMING OF SARS-COV-2 INTRODUCTIONS INTO WASHINGTON STATE,*Diana Tordoff
8:55 AM Break
Session 7 - Bioinformatics & Analysis Methods for SARS-CoV-2  
Session Chairs: Denise Kuehnert & Katrina Lythgoe
9:10 AM RAPID GENOME-BASED ESTIMATION OF SARS-COV-2 INCIDENCE, *Max von Kleist
9:20 AM STABILITY OF SARS-COV-2 PHYLOGENIES, *Bryan Thornlow
9:30 AM IDENTIFICATION OF SARS-COV-2 RECOMBINANT GENOMES,*David VanInsberghe
9:40 AM OPTIMIZING VIRAL GENOMES SUBSAMPLING BY GENOMIC DIVERSITY AND TEMPORAL DISTRIBUTION, *Simone Marini
9:50 AM ULTRAFAST SAMPLE PLACEMENT ON EXISTING TREES (USHER) ENPOWERS REAL-TIME PHYLOGENETICS FOR THE SARS-COV-2 PANDEMIC, *Yatish Turakhia
10:00 AM VIRALMSA: MASSIVELY SCALABLE REFERENCE-GUIDED MULTIPLE SEQUENCE ALIGNMENT OF VIRAL GENOMES, *Niema Moshiri
10:10 AM Break
Session 8 - Modeling within-host dynamics of SARS-CoV-2
Session Chairs: Libin Rong & Mary Bushman
10:25 AM

THE IMPACT OF SARS-COV-2 VIRAL DYNAMICS ON POPULATION LEVEL SPREAD, SUPER-SPREADER EVENTS, AND OPTIMIZATION OF MASKING AND ANTIVIRAL THERAPY, *Ashish Goyal

10:45 AM KINETICS OF SARS-COV-2 INFECTION IN THE HUMAN UPPER AND LOWER RESPIRATORY TRACTS AND THEIR RELATIONSHIP WITH INFECTIOUSNESS, *Ruian Ke
11:00 AM MODELING SARS-COV-2 VIRAL KINETICS AND ASSOCIATION WITH MORTALITY IN HOSPITALIZED PATIENTS RESULTS FROM THE FRENCH COVID-19, *Guillame Lingas
11:15 AM RKI_COVIDTESTCALCULATOR: A STANDALONE GUI TO ASSESS TESTING- AND QUARANTINE STRATEGIES FOR INCOMING TRAVELERS, CONTACT PERSON MANAGEMENT AND DE-ISOLATION, *Max Von Kleist & Wiep van der Toor
11:30 AM A PROTOTYPE QSP MODEL OF THE IMMUNE RESPONSE TO SARS-CoV-2 FOR COMMUNITY DEVELOPMENT, *Rohit Rao
11:45 AM A COALITION-DRIVEN EFFORT TO MODEL SARS-COV-2 SPREAD AND IMMUNE RESPONSE IN TISSUE, *Paul Macklin
12:00 PM

SYSTEMIC AND TISSUE-LEVEL QUANTITATIVE MODELLING DISTINGUISHES THE IMMUNE RESPONSE TO SARS-COV-2, *Adrianne Jenner

12:15 PM

Closing Remarks

Agenda last updated: October 20, 2020


Posters

  1. CAPTURING 35 NATIONAL SCHOOL CLOSURE INTERVENTIONS IN A MODEL OF COVID-19 DIAGNOSES AND DEATHS, *R. Belew
  2. HIGH-DENSITY AMPLICON SEQUENCING IDENTIFIES COMMUNITY SPREAD AND ONGOING EVOLUTION OF SARS-COV-2 IN THE SOUTHERN UNITED STATES, *J. Landis
  3. HOSPITAL CAPACITY AND COVID-19 MORTALITY, *M. Alkuzweny
  4. APPROPRIATE APPROACHES TO ESTIMATE THE EARLY EPIDEMIC GROWTH RATE AND THE REPRODUCTIVE NUMBER R0 OF SARS-COV-2 AND IMPLICATIONS FOR VACCINATION, *R. Ke
  5. SARS-COV-2 GENOMIC AND QUASISPECIES ANALYSES IN CANCER PATIENTS REVEAL RELAXED INTRAHOST VIRUS EVOLUTION, *L. Goes
  6. EFFECTIVENESS OF MASSIVE TRAVEL RESTRICTIONS ON MITIGATING OUTBREAKS OF COVID-19 IN CHINA, *X. Chen
  7. LINEAGE-LEVEL DIVERSIFICATION RATES REFLECT LONGITUDINAL CHANGES IN COVID-19 EPIDEMIC CHARACTERISTICS, *R. Miller
  8. VARIABLE ROUTES TO GENOMIC AND HOST ADAPTATION AMONG CORONAVIRUSES, *V. Montoya
  9. PHYLODYNAMIC ANALYSES SUPPORT THE ASSOCIATION OF THE INITIAL EXPANSION OF A LARGE SARS-COV-2 LINEAGE (A.2) TO A FUNERAL IN NORTHERN SPAIN, *M. Thomson
  10. Withdrawn
  11. WRONG PERSON, PLACE, AND TIME: VIRAL LOAD AND CONTACT NETWORK STRUCTURE PREDICT SARS-COV-2 TRANSMISSION AND SUPER-SPREADING EVENTS, *B. Mayer
  12. ESTIMATING THE STATE OF THE COVID-19 EPIDEMIC IN FRANCE USING A NON-MARKOVIAN MODEL, *R. Forien
  13. ESTIMATING DATES OF ORIGIN AND END OF COVID-19 EPIDEMICS: THE IMPORTANCE OF STOCHASTIC DYNAMICS AND MEMORY EFFECTS, *T. Beneteau
  14. MASK MEDIATED REDUCTION OF EXPOSURE VIRAL LOAD MAY RESULT IN REDUCTION OF SARS-COV-2 TRANSMISSION,  *F. Cardozo-Ojeda
  15. A NETWORK SEIR MODEL: QUARANTINE EFFECTS AND GENETIC EVOLUTION, *V. Marquioni
  16. PROCESS MEMORY IS KEY TO CAPTURING COVID-19 EPIDEMIOLOGICAL DYNAMICS, *S. Alizon
  17. CONTROLLING COVID-19 VIA TEST-TRACE-QUARANTINE, *C. Kerr
  18. INDIVIDUAL HETEROGENEITY IN DISEASE OUTBREAK MODELLING, *B. Elie
  19. ESTIMATION OF SARS-COV-2 MORTALITY DURING THE EARLY STAGES OF AN EPIDEMIC: A MODELING STUDY IN HUBEI, CHINA, AND SIX REGIONS IN EUROPE, *A. Hauser
  20. HOSPITAL DEMAND UNDER INTERVENTION DURING THE COVID-19 PANDEMIC : A MODELING STUDY, *K. Hayashi
  21. TIME TREND OF CASE FATALITY RISK OF COVID-19 IN JAPAN, *T. Kayano
  22. PHENOMENOLOGICAL AND MECHANISTIC MODEL COMPARISON FOR THE FORECAST OF AN EPIDEMIC USING COVID-19 REPORTED DATA IN CHINA, *T. Miyama
  23. GLOBAL GEOGRAPHIC AND TEMPORAL ANALYSIS OF SARS-COV-2 HAPLOTYPES NORMALIZED BY COVID-19 CASES, *S. Justo Arevalo
  24. SARS-COV-2 ON CAMPUS, MODELING THE EDGE OF FAILURE UNDER ASSUMPTIONS OF CONTACT NUMBER AND COMPLIANCE PARAMETERS, *G. Corey
  25. THE UNINTENDED CONSEQUENCES OF INCONSISTENT PANDEMIC CONTROL POLICIES, *S. Scarpino
  26. VARIATION IN SARS-COV-2 FREE-LIVING SURVIVAL AND ENVIRONMENTAL TRANSMISSION CAN MODULATE THE INTENSITY OF EMERGING OUTBREAKS, *S. Scarpino
  27. ASSESSING LINKED SELECTION AND LONG-DISTANCE ASSOCIATIONS OF FUNCTIONAL MUTATIONS IN SARS-COV2 VARIANTS IN INDIA, *I. Singh Rawal
  28. CROWDING AND THE SHAPE OF COVID-19 EPIDEMICS, *S. Scarpino
  29. APPLYING V-PIPE TO SARS-COV-2, *I. Topolsky
  30. RECONSTRUCTING THE EARLY GLOBAL DYNAMICS OF UNDER-ASCERTAINED COVID-19 CASES AND INFECTIONS, *T. Russel
  31. EPIDEMIOLOGICAL MODELING OF COVID-19 DEATH RATE EXPLAINS PERVERSE MOBILITY-MORTALITY CORRELATION, *D. Lewis
  32. GENOMIC EPIDEMIOLOGY OF THE EARLY STAGES OF SARS-COV-2 OUTBREAK IN RUSSIA, *G. Bazykin
  33. DIFFERING IMPACTS OF GLOBAL AND REGIONAL RESPONSES ON SARS-COV-2 TRANSMISSION CLUSTER DYNAMICS, *B. Rife Magalis
  34. FEASIBILITY OF CONTAINING COVID-19 BY SYMPTOM BASED CASE ISOLATION, * R. Kinoshita
  35. NEXT GENERATION MATRIX OF COVID-19 BY OCCUPATION IN JAPAN, *H. Nishiura
  36. OPTIMISING TIME-LIMITED NON-PHARMACEUTICAL INTERVENTIONS FOR COVID-19 OUTBREAK CONTROL, *A. Morgan

Conference Chairs

Alison Hill, PhD

Alison Hill, PhD
Harvard University

Emma Hodroft, PhD

Emma Hodroft, PhD
Postdoctoral Fellow
University of Basel

Morgane Rolland, PhD

Morgane Rolland, PhD
US Military HIV Research Program


Syllabus

Download syllabus (7.7mb pdf)

green cmeThe abstract book will be available electronically. A link will be emailed to all registered attendees prior to the October 19-20 meeting.

The abstract book will be available for download on the conference website approximately (1) one week after the conference.

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